I recommend that you create the custom menus in the template either via VBA or manually customizing the menus, rather than through your external executable.

My best practices recommendation (fwiw) is to use a macro to create your custom menus.  If the menus are dynamic (depend on document content, for example), you'll want to call the menu creation macro every time a document attached to the template opens.  If the menus are static, then just run the macro once, save the template, and don't re-run the macro again unless you're re-generating the whole template (which is recommended to do every once in awhile to reduce template bloat).
Using a macro to generate custom menu items allows you to quickly and easily change them, or generate them fresh.

If you're going to dynamically generate your custom menus for each document, then wrap your menu-generation calls with
Application.CustomizationContext = ActiveDocument.AttachedTemplate
and
ActiveDocument.AttachedTemplate.Saved = True

That will ensure that your menu changes end up in the template, not in the document, and that the "do you want to save changes to the document template?" prompt won't display.

Example:

Dim oPrint As CommandBarButton

' include with dynamic custom menus
Application.CustomizationContext = ActiveDocument.AttachedTemplate

With Application.CommandBars.Add("MyBar", msoBarTop, , True)
   .Enabled = True
   .Visible = True
   With .Controls
     Set oPrint = .Add(Type:=msoControlButton)
     With oPrint
       .Caption = "Special &Print"
       .FaceId = 176
       .Style = msoButtonIconAndCaption
       .OnAction = "Module1.SpecialPrint"
       .TooltipText = "Special Print"
       .Enabled = True
       .Visible = True
       .Priority = 1
     End With
   End With
End With

' include with dynamic custom menus
ActiveDocument.AttachedTemplate.Saved = True

hth,

-Peter